RetrogeneDB ID: retro_pabe_804

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 11:116790440..116791354(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: DDX39B
• Ensembl ID: ENSPPYG00000016433
• Aliases: None
• Description: Spliceosome RNA helicase DDX39B [Source:UniProtKB/Swiss-Prot;Acc:Q5RE47]

Sequence

>retro_pabe_804
CTTCTGCTCCTCCACTCTGGGGAACAGGCGCTGTTGGCTTCCCAAGCCATGGTCAGTTCTCTAAATACATGCCCAGTGTC
AAGGTTGCTGTGTTTTTTGGTGGTCTATCAAGAAGGATGAAGAGGTGCTGAAGAACTGCCTGCATATCATCGTGGGGACT
CCAGGCCGTATCCTAGCCCTGGCTGGCAATAAGAGCCTCAACCTCAAACACATAAAACACTTTATTTCGAATGAATGTGA
TAAGACGTTTGAACAGCTCAACATGTGTCGGGATGTCCAGGGAATTTTTCACATGACCCCACCGTGAGAAGCCGGTCATG
ATGTTGAGGGCTACCTTGAGCAAAGAGATCCGTCCAGTCTGCCACAAGTTCATGCAAGATCCAGTGGAGATCTTTGTGGA
TAATGAGATGAAGTTGATGCTGCATGGGTTGCAGCAGTACTACATGAAACTGAAGGACAACCAGAAGAACTGGAAGCTCT
ATGACCTTCTGAATGTCCTTGAGTTCAACCAGGTGATGATCTTTTTGAAGTCTGTGCAGTGGCGCATTGCCTCGGCCCAG
CTACTGGATAGAGCAGAACTTCCCAGCCATTGCCATCCACTACGGAATGCCCCAGGGCAGAGGCTCTCTCAGTATCAGCA
GTTTAAAGATTTTCAGTGGTGAATTCTTGTGGCTACCAACATATTTGGCCAAAGAATGGACATTGAGTGGGTGAACATTG
CTTTTAATGATGACATACCTGAGGATTCTGACACCTACCTGCATTGGGTGGCCAGAGCCAGCCGGTTTGGCACCAAGGGC
TTGGCTATCACATTTGTGTCTGACGAGAATGATGCCAAGATCCTCAATGACATGCAGGATCGCTTTGAGGTCAATCGCAG
TGATCTGCCTGATGAGAGAGACATCTTCTCCTAC

Alignment

ORF - retro_pabe_804 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.96 %
• Parental protein coverage: 71.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LVMCHTRELAFQISK-EYERFSKYMPNVKVAVFFGGLS-IKKDEEVLKKNCPHIVVGTPGRILALARNKS
          L...H..E.A...S......FSKYMP.VKVAVFFGGLS..K..E.VLK.NC.HI.VGTPGRILALA.NKS
Retrocopy LLLLHSGEQALLASQ<SHGQFSKYMPSVKVAVFFGGLS<KKDEE-VLK-NCLHIIVGTPGRILALAGNKS

Parental  LNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTP-HEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDD
          LNLKHIKHFI..ECDK..EQL.M.RDVQ.IF.MTP..EK.VMM..ATLSKEIRPVC.KFMQDP.EIFVD.
Retrocopy LNLKHIKHFISNECDKTFEQLNMCRDVQGIFHMTP>REKPVMMLRATLSKEIRPVCHKFMQDPVEIFVDN

Parental  ETKLTLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLL-VEQNFPAIAIHRGMP
          E.KL.LHGLQQYY.KLKDN.KN.KL.DLL.VLEFNQV.IF.KSVQ..IA.AQLL..EQNFPAIAIH.GMP
Retrocopy EMKLMLHGLQQYYMKLKDNQKNWKLYDLLNVLEFNQVMIFLKSVQWRIASAQLL>IEQNFPAIAIHYGMP

Parental  Q-EERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFV
          Q...RLS.YQQFKDFQ..ILVATN.FG..MDIE.VNIAFN.D.PEDSDTYLH.VARA.RFGTKGLAITFV
Retrocopy Q<GQRLSQYQQFKDFQW*ILVATNIFGQRMDIEWVNIAFNDDIPEDSDTYLHWVARASRFGTKGLAITFV

Parental  SDENDAKILNDVQDRFEVNISELPDEIDISSY
          SDENDAKILND.QDRFEVN.S.LPDE.DI.SY
Retrocopy SDENDAKILNDMQDRFEVNRSDLPDERDIFSY

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	94.44 RPM
SRP007412_cerebellum	0.00 RPM	185.44 RPM
SRP007412_heart	0.00 RPM	68.21 RPM
SRP007412_kidney	0.07 RPM	150.02 RPM
SRP007412_liver	0.00 RPM	120.48 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_804 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_804 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_804 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_752
Macaca mulatta	retro_mmul_1126

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003152	1 retrocopy	retro_cjac_1461,
Macropus eugenii	ENSMEUG00000008264	2 retrocopies	retro_meug_1623, retro_meug_288,
Macaca mulatta	ENSMMUG00000008839	1 retrocopy	retro_mmul_1126,
Pongo abelii	ENSPPYG00000016433	1 retrocopy	retro_pabe_804 ,